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A portable and fast single cell type identifier
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Error in DsGene(expr, labels_in, as_df, k, 0, n_threads) : std::bad_alloc #7

Open levinhein opened 4 years ago

levinhein commented 4 years ago

Hi. I encounter an error when I run the SelectGene() function. 

> etest_gene <- SelectGene(expressionmatrix, k = 50)
Error in DsGene(expr, labels_in, as_df, k, 0, n_threads) : std::bad_alloc

image

How to resolve this?

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_PH.UTF-8       LC_NUMERIC=C               LC_TIME=en_PH.UTF-8        LC_COLLATE=en_PH.UTF-8    
 [5] LC_MONETARY=en_PH.UTF-8    LC_MESSAGES=en_PH.UTF-8    LC_PAPER=en_PH.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_PH.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggsci_2.9         viridis_0.5.1     viridisLite_0.3.0 scibet_1.0        tibble_3.0.4      tidyr_1.1.2       data.table_1.13.2
 [8] Matrix_1.2-18     patchwork_1.0.1   ggplot2_3.3.2     cowplot_1.1.0     dplyr_1.0.2       Seurat_3.2.2     

loaded via a namespace (and not attached):
 [1] nlme_3.1-149          matrixStats_0.57.0    RcppAnnoy_0.0.16      RColorBrewer_1.1-2    httr_1.4.2           
 [6] sctransform_0.3.1     tools_4.0.3           R6_2.4.1              irlba_2.3.3           rpart_4.1-15         
[11] KernSmooth_2.23-17    uwot_0.1.8            lazyeval_0.2.2        mgcv_1.8-33           colorspace_1.4-1     
[16] withr_2.3.0           tidyselect_1.1.0      gridExtra_2.3         compiler_4.0.3        plotly_4.9.2.1       
[21] scales_1.1.1          lmtest_0.9-38         spatstat.data_1.4-3   ggridges_0.5.2        pbapply_1.4-3        
[26] rappdirs_0.3.1        spatstat_1.64-1       goftest_1.2-2         stringr_1.4.0         digest_0.6.26        
[31] spatstat.utils_1.17-0 pkgconfig_2.0.3       htmltools_0.5.0       fastmap_1.0.1         htmlwidgets_1.5.2    
[36] rlang_0.4.8           rstudioapi_0.11       shiny_1.5.0           generics_0.0.2        zoo_1.8-8            
[41] jsonlite_1.7.1        ica_1.0-2             magrittr_1.5          Rcpp_1.0.5            munsell_0.5.0        
[46] abind_1.4-5           reticulate_1.17       lifecycle_0.2.0       stringi_1.5.3         MASS_7.3-53          
[51] Rtsne_0.15            plyr_1.8.6            grid_4.0.3            parallel_4.0.3        listenv_0.8.0        
[56] promises_1.1.1        ggrepel_0.8.2         crayon_1.3.4          miniUI_0.1.1.1        deldir_0.1-29        
[61] lattice_0.20-41       splines_4.0.3         tensor_1.5            pillar_1.4.6          igraph_1.2.6         
[66] future.apply_1.6.0    reshape2_1.4.4        codetools_0.2-16      leiden_0.3.3          glue_1.4.2           
[71] png_0.1-7             vctrs_0.3.4           httpuv_1.5.4          gtable_0.3.0          RANN_2.6.1           
[76] purrr_0.3.4           polyclip_1.10-0       future_1.19.1         rsvd_1.0.3            mime_0.9             
[81] xtable_1.8-4          later_1.1.0.1         survival_3.2-7        cluster_2.1.0         globals_0.13.1       
[86] fitdistrplus_1.1-1    ellipsis_0.3.1        ROCR_1.0-11
evenDDDDD commented 3 years ago

Hi! Unfortunately, I also encountered the same mistake as you. Did you solve it？